Hello all,
With a cuffmerge result (into ./cufflinks_all/merged.gtf), I am trying to cuffcompare it against a reference gtf (../public/publicCuffMergedLncProts/merged.gtf) as follows:
[...]$ cuffcompare -V -o ./testOut -r ../public/publicCuffMergedLncProts/merged.gtf -C ./cufflinks_all/merged.gtf
You are using Cufflinks v2.1.1, which is the most recent release.
Loading reference transcripts..
..reference annotation loaded
Prefix for output files: testOut
Processing qfile #1: ./cufflinks_all/merged.gtf
Loading transcripts from ./cufflinks_all/merged.gtf..
462 redundant cufflinks transfrags discarded.
Found 15380 transcripts with undetermined strand.
Tracking transcripts across 1 query files..
Cleaning up..
Done.
But after all this, nothing happens.
Of course, there are much more transcripts with determined strand (468,928).
Have you ever had this kind of situation?
Thanks in advance!
HJ.
With a cuffmerge result (into ./cufflinks_all/merged.gtf), I am trying to cuffcompare it against a reference gtf (../public/publicCuffMergedLncProts/merged.gtf) as follows:
[...]$ cuffcompare -V -o ./testOut -r ../public/publicCuffMergedLncProts/merged.gtf -C ./cufflinks_all/merged.gtf
You are using Cufflinks v2.1.1, which is the most recent release.
Loading reference transcripts..
..reference annotation loaded
Prefix for output files: testOut
Processing qfile #1: ./cufflinks_all/merged.gtf
Loading transcripts from ./cufflinks_all/merged.gtf..
462 redundant cufflinks transfrags discarded.
Found 15380 transcripts with undetermined strand.
Tracking transcripts across 1 query files..
Cleaning up..
Done.
But after all this, nothing happens.
Of course, there are much more transcripts with determined strand (468,928).
Have you ever had this kind of situation?
Thanks in advance!
HJ.
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